Serine proteases and their homologs in the Drosophila melanogaster genome: an initial analysis of sequence conservation and phylogenetic relationships

• Published in: Gene Vol. 304; no. C; pp. 117 - 131
• Main Authors: Ross, Jeremy, Jiang, Haobo, Kanost, Michael R, Wang, Yang
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 30.01.2003
• Subjects: Amino Acid Sequence; Animals; Catalytic Domain - genetics; Chromosome Mapping; Clip domain; Conserved Sequence - genetics; Databases, Protein; Drosophila melanogaster - enzymology; Drosophila melanogaster - genetics; Drosophila Proteins - genetics; Expressed Sequence Tags; Genome; Insect immunity; Molecular Sequence Data; Phylogenetic analysis; Phylogeny; Sequence Alignment; Sequence Homology, Amino Acid; Serine Endopeptidases - genetics; Serine protease homolog; SP, serine proteinase; SPH, serine protease homolog; EST, expressed sequence tag; Phylogenetic analysis; Clip domain; c-SPH, clip-domain serine protease homolog; NCBI, National Center for Biotechnology Information; cDNA, DNA complementary to RNA; PAP, prophenoloxidase activating protease; Insect immunity; c-SP, clip-domain serine protease; Serine protease homolog; PSI-BLAST, position-specific iterated basic local alignment search tool
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/S0378-1119(02)01187-3

Serine proteases (SPs) and serine protease homologs (SPHs) constitute the second largest family of genes in the Drosophila melanogaster genome. Eighty-four SPs comprise less than 300 amino acid residues, and a significant portion of them are probably digestive enzymes. Some larger SPs may contain one or more regions important for protein–protein interactions, including clip domains, low-density lipoprotein receptor class A repeats, and scavenger receptor cysteine-rich domains. We identified 37 clusters of SP or SPH genes, which probably evolved from relatively recent gene duplication and sequence divergence. A majority of the SPs may be trypsin-like and activated by cleavage after a specific arginine or lysine residue. Among the 147 SPs and 57 SPHs studied, 24 SPs and 13 SPHs contain at least one regulatory clip domain. A multiple sequence alignment of the clip domains provided further information on structural conservation of these regulatory modules. Detailed sequence comparison led to an improved classification system for SPs containing clip domains. These analyses have established a framework of information about evolutionary relationships among the Drosophila SPs and SPHs, which may facilitate research on these proteins as well as homologous molecules from other invertebrate species.